Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers—ITS1, ITS2, 18S V4–V5 and 28S D1–D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding—a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.

How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on local fungal species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). We integrate fungi into the principles of global biodiversity distribution and present detailed maps for biodiversity conservation and modeling of global ecological processes.

Pesticides are widely distributed in soils ^1–3 , yet their effects on soil biodiversity remain poorly understood ^4–7 . Here we examined the effects of 63 pesticides on soil archaea, bacteria, fungi, protists, nematodes, arthropods and key functional gene groups across 373 sites spanning woodlands, grasslands and croplands in 26 European countries. Pesticide residues were detected in 70% of sites and emerged as the second strongest driver of soil biodiversity patterns after soil properties. Our analysis further revealed organism- and function-specific patterns, emphasizing complex and widespread non-target effects on soil biodiversity. Pesticides altered microbial functions, including phosphorus and nitrogen cycling, and suppressed beneficial taxa, including arbuscular mycorrhizal fungi and bacterivore nematodes. Our findings highlight the need to integrate functional and taxonomic characteristics into future risk assessment methodology to safeguard soil biodiversity, a cornerstone of ecosystem functioning.

Mycorrhizal fungi are ecosystem engineers that sustain plant life and help regulate Earth's biogeochemical cycles^1-3. However, in contrast to plants and animals, the global distribution of mycorrhizal fungal biodiversity is largely unknown, which limits our ability to monitor and protect key underground ecosystems^4,5. Here we trained machine-learning algorithms on a global dataset of 25,000 geolocated soil samples comprising >2.8 billion fungal DNA sequences. We predicted arbuscular mycorrhizal and ectomycorrhizal fungal richness and rarity across terrestrial ecosystems. On the basis of these predictions, we generated high-resolution, global-scale maps and identified key reservoirs of highly diverse and endemic mycorrhizal communities. Intersecting protected areas with mycorrhizal hotspots indicated that less than 10% of predicted mycorrhizal richness hotspots currently exist in protected areas. Our results describe a largely hidden component of Earth's underground ecosystems and can help identify conservation priorities, set monitoring benchmarks and create specific restoration plans and land-management strategies.

Molecular analyses of soil and water commonly reveal large proportions of fungal taxa that cannot be assigned to any taxonomic or functional groups. Some of these so-called dark taxa have been encoded alphanumerically, while others have remained completely overlooked. Using long-read sequencing that covers much of the ribosomal RNA operon, we shed light on the phylogenetic and ecological distribution of fungal dark taxa and formally describe 30 of the most prominent phylum- to order-level lineages based on their characteristic DNA features. This increases the known large-scale fungal phylogenetic diversity by roughly one-third. Formal names will enhance taxonomic reproducibility, facilitate communication among researchers, and enable the estimation of conservation and quarantine needs for uncultivable species and higher-ranking taxa. The new species in the respective highest-level novel taxonomic groups include Pantelleria saittana (Pantelleriomycetes), Paraspizellomyces parrentiae (Paraspizellomycetales), Aquieurochytrium lacustre (Aquieurochytriomycetes), Edaphochytrium valuojaense (Edaphochytriomycetes), Tibetochytrium taylorii (Tibetochytriomycetes), Tropicochytrium toronegroense (Tropicochytriomycetes), Algovorax scenedesmi (comb. nov.) and Solivorax pantropicus (Algovoracomycetes), Aquamastix sanduskyensis (Aquamastigomycetes), Cantoromastix holarctica (Cantoromastigomycetes), Dobrisimastix vlkii (Dobrisimastigomycetes), Palomastix lacustris (Palomastigomycetes), Sedimentomastix tueriensis (Sedimentomastigomycetes), Terrincola waldropii (Terrincolales), Curlevskia holarctica (Curlevskiomycota), Mycosocceria estonica (Mycosocceriales), Maerjamyces jumpponenii (Maerjamycetes), Ruderalia cosmopolita (Ruderaliomycetes), Bryolpidium mundanum (Bryolpidiomycetes), Chthonolpidium enigmatum (Chthonolpidiomycetes), Savannolpidium raadiense (Savannolpidiomycetes), Gelotisporidium boreale (Gelotisporidiomycetes), Sumavosporidium sylvestre (Sumavosporidiomycetes), Parakickxella borikenica (Parakickxellomycetes), Aldinomyces tarquinii (Aldinomycota), Borikenia urbinae (Borikeniomycota), Mirabilomyces abrukanus (Mirabilomycota), Nematovomyces vermicola (comb. nov.) and N. soinasteënsis (Nematovomycota), Viljandia globalis (Viljandiomycota), Waitukubulimyces cliftonii (Waitukubulimycota), and Tartumyces setoi (Tartumyceta).